taxonomic classification with rna-seq data

Question

[vm.higareda]

I have some single end RNA-seq data from Drosophila larvae and I would like to know what other microorganisms are present in my samples different to Drosophila.

Do you have any recommendation? I have read that kraken can do taxonomic classification with RNA-seq and also IMSA+A.

My RNA-seq libraries were not polyA enriched and I have a considerable number of reads that do not map to D. melanogaster genome.

[GenoMax]

Kraken2 and Kaiju are a couple of programs you could use for microbial classification.

As for the reads that do not map you could take a sampleof non-mapping reads and do a quick blast search at NCBI. Hopefully any contamination is with one or two species and can be readily identified. If you have substantial contamination with non-expected species then the entire experiment may need to be reviewed for usability.